Eren couldn't read Maya's thoughts even with his soul sense.
That's because she didn't have a soul, to begin with. Maya's artificial intelligence came from Sage Lehan's array algorithm– something that was planted deep inside her.
As a result, Eren's soul sense wasn't able to decipher her thoughts. According to his soul sense, Maya hovered between life and death. But she was unlike the undead he was used to summoning.
Undead were once living beings that had either been forced to or wanted to be part of life. As such, they had vestiges of their souls embedded in them no matter how insignificant.
Maya on the other hand seemed like an already dead entity that had managed to knock on life's door. She didn't have any vestige of a soul attached to her even if her body was lifelike. It was as if her body was kept alive by a different source than the source of life.
